The genomic signature of dog domestication reveals adaptation to a starch-rich diet

Mikk Eelmets Journal Club 25.03.2013 Canis lupus familiaris

Canis lupus Fossilised dog remains 33,000-year-old doglike canid from the Altai Mountains in Siberia 12,000– 11,000 years BP found buried together with humans in Israel could represent the earliest verified dog remains

Patterns of genomic variation indicate that dog domestication started at least 10,000 years BP in southern East Asia or the Middle East Sequencing

• 12 wolves, 60 dogs (14 diverse breeds) • 12 individuals per pool • AB SOLiD ver3 (mate-pair) • Aligned to CanFam 2.0 reference • Bioscope 1.1 • 3.79M SNP, 0.51M Indels, 26619 CNVs • Unique for dogs 1.77M SNPs, for wolf 0.14M SNPs

Distribution of sequence coverage for the five dog pools combined and a single wolf pool Selection signals

• pooled heterozygosity (Hp)

• fixation index (FST) Selection signals

a. Distribution of Z-transformed average pooled heterozygosity in dog (Z(Hp)DOG) and wolf (Z(Hp)WOLF) respectively, as well as average fixation index (Z(FST)), for autosomal 200 kb windows (σ, standard deviation; µ, average) b. The positive end of the Z(Fst) distribution plotted along dog autosomes 1–38 ( are separated by colour). A dashed horizontal line indicates the cut-off (Z > 5) used for extracting outliers. c. The negative end of the Z(Hp) distribution plotted along dog autosomes 1–38. A dashed horizontal line indicates the cut-off (Z < −5) used for extracting outliers. Selection signals

• 36 unique autosomal candidate domestication region (CDR) • 122 • Overrepresented ontology terms in 25 categories, representing several groups of interrelated terms (nervous system development, sperm-egg recognition, digestion, regulation of molecular function)

Starch metabolism in dogs

• Three stages: 1. starch is first cleaved to maltose and other oligosaccharides by alpha- in the intestine; 2. the oligosaccharides are subsequently hydrolysed by maltase-glucoamylase, sucrase and isomaltase to form glucose; 3. glucose is transported across the plasma membrane by brush border protein SGLT1 a. Pooled heterozygosity, Hp (blue), and average fixation index, Fst (orange), plotted for 200-kb windows across a 6 region harbouring AMY2B b. Heterozygosity, Hp (blue), and fixation index, Fst (orange), for single SNPs in the selected region. Dog relative to wolf coverage, rC (green line), indicates increase in AMY2B copy number in dog. Genes in the region are shown below panel c. Histogram showing the distribution of diploid amylase copy number in wolf (n = 35) (blue) and dog (n = 136) (red) d. Amylase messenger RNA expression levels in pancreas of wolf (n = 12) and dog (n = 9). e. Amylase activity in serum from wolf (n = 13) and dog (n = 12). a. Pooled heterozygosity, Hp (blue), and average fixation index, Fst (orange), plotted for 200-kb windows across a chromosome 16 region harbouring MGAM b. Heterozygosity, Hp (blue), and fixation index, Fst (orange), for single SNPs in the selected region c. Haplotypes inferred from genotyping of 47 SNPs across the MGAM locus in 71 dogs and 19 wolves (red and blue colour are major and minor dog allele, respectively). Genes in the genotyped region are shown below panel. d. MGAM mRNA expression levels in pancreas of wolf (n = 8) and dog (n = 9). e. MGAM activity in serum from wolf (n = 8) and dog (n = 7). a. Pooled heterozygosity, Hp (blue dots), and average fixation index, Fst (orange dots) plotted for 200 Kb windows across a region spanning 20-35 Mb on chromosome 26. Dashed vertical lines indicate the location of the selected region harbouring SGLT1. b. Magnification of the region affected by selection showing heterozygosity, H (blue dots) and fixation index, FST (orange dots) estimated for single SNPs. Dashed horizontal lines delineate genotyped region shown in panel c c. Haplotypes inferred from genotyping of 48 SNPs in 71 dogs and 19 wolves, shows the location of a 50.5 Kb region, spanning approximately 27.96-28.01 Mb, that is nearly fixed in all dogs. Red colour represents the major dog allele, while blue is minor dog allele. Genes residing in the genotyped region are shown below panel c. Conclusion

• Dog domestication was accompanied by selection at three genes with key roles in starch digestion: AMY2B, MGAM and SGLT1 • This may suggest that a change of ecological niche (adaptations to thrive on a diet rich in starch) could have been the driving force behind the domestication process Reference

E. Axelsson et al. " The genomic signature of dog domestication reveals adaptation to a starch-rich diet. “ Nature 495, 360–364 (2013) THANK YOU